bool FileIntersect::processUnsortedFiles()
{
const QuickString &databaseFilename = _context->getDatabaseFileName();
BinTree *binTree = new BinTree(_context->getDatabaseFileIdx(), _context);
FileRecordMgr *queryFRM = new FileRecordMgr(_context->getQueryFileIdx(), _context);
if (!queryFRM->open()) {
return false;
}
if (!binTree->loadDB()) {
fprintf(stderr, "Error: Unable to load database file %s.\n", databaseFilename.c_str());
delete binTree;
exit(1);
}
_context->determineOutputType();
_recordOutputMgr->init(_context);
while (!queryFRM->eof()) {
Record *queryRecord = queryFRM->allocateAndGetNextRecord();
if (queryRecord == NULL) {
continue;
}
RecordKeyList hitSet(queryRecord);
binTree->getHits(queryRecord, hitSet);
if (_context->getObeySplits()) {
RecordKeyList keySet(hitSet.getKey());
RecordKeyList resultSet;
_blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
processHits(resultSet);
} else {
processHits(hitSet);
}
queryFRM->deleteRecord(queryRecord);
}
queryFRM->close();
//clean up.
delete queryFRM;
delete binTree;
return true;
}
bool ContextBase::openFiles() {
//Make a vector of FileRecordMgr objects by going through the vector
//of filenames and opening each one.
if (_allFilesOpened) {
return true;
}
if (_fileNames.size() == 0) {
//No input was specified. Error and exit.
_errorMsg += "\n***** ERROR: No input file given. Exiting. *****";
return false;
}
_files.resize(_fileNames.size());
for (int i = 0; i < (int)_fileNames.size(); i++) {
FileRecordMgr *frm = getNewFRM(_fileNames[i], i);
if (hasGenomeFile()) {
frm->setGenomeFile(_genomeFile);
}
//If we're going to do column operations, and an input file
// is BAM, we'll need the full flags.
if (hasColumnOpsMethods()) {
setUseFullBamTags(true);
}
frm->setFullBamFlags(_useFullBamTags);
frm->setIsSorted(_sortedInput);
frm->setIoBufSize(_ioBufSize);
frm->setIsGroupBy(_program == GROUP_BY);
if (!frm->open(_inheader)) {
return false;
}
if (_noEnforceCoordSort) {
frm->setNoEnforceCoodSort(true);
}
_files[i] = frm;
}
_allFilesOpened = true;
return true;
}
bool ContextBase::openFiles() {
//Make a vector of FileRecordMgr objects by going through the vector
//of filenames and opening each one.
if (_allFilesOpened) {
return true;
}
_files.resize(_fileNames.size());
for (int i = 0; i < (int)_fileNames.size(); i++) {
FileRecordMgr *frm = new FileRecordMgr(_fileNames[i], _sortedInput);
if (hasGenomeFile()) {
frm->setGenomeFile(_genomeFile);
}
frm->setFullBamFlags(_useFullBamTags);
if (!frm->open()) {
return false;
}
_files[i] = frm;
}
_allFilesOpened = true;
return true;
}
